Incomplete lineage sorting and local extinction shaped the complex evolutionary history of the Paleogene relict conifer genus, Chamaecyparis (Cupressaceae).

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Publisher: Elsevier B.V.
Document Type: Report
Length: 465 words

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Keywords Chamaecyparis; Cytonuclear discordance; East Asia-North America disjunction distribution; HybPiper; Incomplete lineage sorting Highlights * A well-resolved species tree of Chamaecyparis was constructed using target enrichment sequencing of multiple individuals per species for the first time. * Cytonuclear discordance and conflicting topologies between nuclear gene trees were detected. * Incomplete lineage sorting is the major contributor to the observed phylogenetic discrepancies. * Chamaecyparis is a Paleogene relict genus of the "boreotropical" flora. Abstract Inferring accurate biogeographic history of plant taxa with an East Asia (EA)-North America (NA) is usually hindered by conflicting phylogenies and a poor fossil record. The current distribution of Chamaecyparis (false cypress; Cupressaceae) with four species in EA, and one each in western and eastern NA, and its relatively rich fossil record, make it an excellent model for studying the EA-NA disjunction. Here we reconstruct phylogenomic relationships within Chamaecyparis using 1400 homologous nuclear and 61 plastid genes. Our phylogenomic analyses using concatenated and coalescent approaches revealed strong cytonuclear discordance and conflicting topologies between nuclear gene trees. Incomplete lineage sorting (ILS) and hybridization are possible explanations of conflict; however, our coalescent analyses and simulations suggest that ILS is the major contributor to the observed phylogenetic discrepancies. Based on a well-resolved species tree and four fossil calibrations, the crown lineage of Chamaecyparis is estimated to have originated in the upper Cretaceous, followed by diversification events in the early and middle Paleogene. Ancestral area reconstructions suggest that Chamaecyparis had an ancestral range spanning both EA and NA. Fossil records further indicate that this genus is a relict of the "boreotropical" flora, and that local extinctions of European species were caused by global cooling. Overall, our results unravel a complex evolutionary history of a Paleogene relict conifer genus, which may have involved ILS, hybridization and the extinction of local species. Author Affiliation: (a) Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, China (b) Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK (c) Institute of Molecular Plant Science, School of Biological Science, University of Edinburgh, Edinburgh EH9 3BF, UK (d) Department of Botany, University of British Columbia, Vancouver, V6T 1Z4, Canada (e) College of Science, Tibet University, Lhasa 850000, Xizang Autonomous Region, PR China * Corresponding author at: Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, China. Article History: Received 1 August 2021; Revised 26 March 2022; Accepted 5 April 2022 (footnote)1 These authors contributed equally. Byline: Yi Wang (a,1), Markus Ruhsam (b,1), Richard Milne (c), Sean W. Graham (d), Jialiang Li (a), Tongzhou Tao (a), Yujiao Zhang (a), Kangshan Mao [maokangshan@scu.edu.cn] (a,e,*)

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Gale Document Number: GALE|A703692409